also some icons are misplaced in Chromium, for example I am not enabling spellcheck

[EDIT]

I had the issue on my local dev environment (Ubuntu LAMP)

When I pushed code to remote site with Git and synced db + files... the icons appeared in the same Chromium browser... hmmm... wtf? I don't think it's permissions, the icons are in two single sprite images

I'm on the same stack, and I'm working on correcting issues like that (in paralell with a lot of other annoying stuff). The buttons-go-off-screen-issues will be solved once button-sorting is completely implemented. (There's an old issue about it somewhere, and a testing branch called sort_buttons - it's a bit behind on d.o still, but I've recently merged in the latest changes from 7.x-2.x locally so I'll push that up to d.o ASAP.) Until then, there's an extra Appearance-setting for CKEditor which tells it to use the default button grouping, which fixes issues like this.